Summer-Chem

Requirement

  1. Python 2.7
  2. Libraries: Biopython 1.69, matplotlib 2.0.2.

For simplicity, use Anaconda to install required libraries.

These scripts here are working with several file formats:

  • Protein Data Bank (PDB) file format: provides a standard representation for macromolecular structure data derived from X-ray diffraction and NMR studies. Proteins of interest can be downloaded at RCSB PDB.
  • probe file format: is generated by Probe software
  • Simple interaction format (SIF) file format: is used for building a graph from a list of interactions. Lines in SIF file specify a source node, a relationship type (or edge type), and one or more target nodes. (Reference: SIF file format - Cytoscape wiki)